Hi Jenny Happy New Year, hope your vacation was good. I'm still having the same problem with the RemoveProbes.r function. basically; I am using the Yeast 2 platform. I have a list of probes which I want to remove (884). I also want to remove all S.pombe probe sets. I am using the latest revision of Remove Probes ( Sept 24, 2008). I am having problems removing more than a certain number of probes at once. This number does not seem to be consistent. To remedy this I am subsetting the list of probes and using the removePobes function more than once. However, this creates problems when I try to run rma. I do not have problems with rma if i run just one instance of remove probes. So I guess the underlying problem is the error that is produced when I try to remove all my 884 probes and the S.pombe probesets at once. Here is all the relevent code ###################################################################### #################################### ### listOutProbes is a character vector containing ###all the cerevisiae probes I wish to remove > listOutProbes[1:5] [1] "1769510_at1" "1769342_at11" "1769383_at6" "1769378_at1" [5] "1769390_s_at4" > > source("RemoveProbesNew.r") > library(yeast2cdf) > library(yeast2probe) > cleancdf <- cleancdfname("yeast2",addcdf=FALSE) > ResetEnvir(cleancdf) Loading required package: yeast2cdf Loading required package: yeast2probe > length(pm(data[,1])) [1] 120855 > RemoveProbes(listOutProbes,listOutProbeSets=pombe_filter_out, cleancdf) Error in ans[[i]][, i.probes] : incorrect number of dimensions > length(pm(data[,1])) Error in x[, 1] : incorrect number of dimensions > ###however if I subset removeprobes like so ###(The first call is the exact limit of what will work, the rest are rough trial and error) ### i.e. listOutProbes[1:233] will work but listOutProbes[1:234] will not. (and it is not a problem with that specific probe) > source("RemoveProbesNew.r") > library(yeast2cdf) > library(yeast2probe) > cleancdf <- cleancdfname("yeast2",addcdf=FALSE) > ResetEnvir(cleancdf) Loading required package: yeast2cdf Loading required package: yeast2probe > length(pm(data[,1])) [1] 120855 > RemoveProbes(listOutProbes[1:233],listOutProbeSets=NULL, cleancdf) > length(pm(data[,1])) [1] 120622 > RemoveProbes(listOutProbes[233:467],listOutProbeSets=NULL, cleancdf) > length(pm(data[,1])) [1] 120389 > RemoveProbes(listOutProbes[467:500],listOutProbeSets=NULL, cleancdf) > length(pm(data[,1])) [1] 120358 > RemoveProbes(listOutProbes[500:600],listOutProbeSets=NULL, cleancdf) > length(pm(data[,1])) [1] 120259 > RemoveProbes(listOutProbes[600:640],listOutProbeSets=NULL, cleancdf) > length(pm(data[,1])) [1] 120221 > RemoveProbes(listOutProbes[640:650],listOutProbeSets=NULL, cleancdf) > length(pm(data[,1])) [1] 120213 > RemoveProbes(listOutProbes[650:700],listOutProbeSets=NULL, cleancdf) > length(pm(data[,1])) [1] 120165 > RemoveProbes(listOutProbes[700:710],listOutProbeSets=NULL, cleancdf) > length(pm(data[,1])) [1] 120158 > RemoveProbes(listOutProbes[710:720],listOutProbeSets=NULL, cleancdf) > length(pm(data[,1])) [1] 120147 > RemoveProbes(listOutProbes[720:800],listOutProbeSets=NULL, cleancdf) > length(pm(data[,1])) [1] 120075 > RemoveProbes(listOutProbes[800:884],listOutProbeSets=NULL, cleancdf) > ### You can see the number of probes in the environment going down with length(pm(data[,1])). ### But even this is not the right number. We should have removed 884 probes but > 120855-120075 [1] 780 ### Here is the traceback() and sessionInfo when I try to remove everything at once > source("RemoveProbesNew.r") > library(yeast2cdf) > library(yeast2probe) > cleancdf <- cleancdfname("yeast2",addcdf=FALSE) > ResetEnvir(cleancdf) Loading required package: yeast2cdf Loading required package: yeast2probe > length(pm(data[,1])) [1] 120855 > RemoveProbes(listOutProbes,listOutProbeSets=pombe_filter_out, cleancdf) Error in ans[[i]][, i.probes] : incorrect number of dimensions > > > traceback() 6: as.vector(ans[[i]][, i.probes]) 5: .local(object, which, ...) 4: indexProbes(newAB, "pm") 3: indexProbes(newAB, "pm") 2: unlist(indexProbes(newAB, "pm")) 1: RemoveProbes(listOutProbes, listOutProbeSets = pombe_filter_out, cleancdf) > > > > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.1252;LC_MONETARY=English_New Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] yeast2probe_2.3.0 yeast2cdf_2.3.0 matchprobes_1.14.0 [4] yeast2.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 [7] AnnotationDbi_1.4.2 affy_1.20.0 Biobase_2.2.1 [10] limma_2.16.3 loaded via a namespace (and not attached): [1] affyio_1.10.1 preprocessCore_1.4.0 > ###################################################################### ######################################### I have also attached an excel file with the names of the probes which I am trying to remove, just in case it helps. Again, many thanks for any help Omri MSc student School of Biological Sciences University of Auckland, New Zealand On Mon, Dec 22, 2008 at 11:21 AM, Omri Yahel <omri.yahel at="" gmail.com=""> wrote: > Hi Jenny > > Thanks for your reply. So sorry to bother you while you're on holiday. I > tried what you told me and it seems the problem is with running RemoveProbes > more than once. I'll send you another e-mail in early January and hopefully > we can sort it out. > Thanks again for you help, I really really appreciate it! > Enjoy your vacation > Omri > > > On Mon, Dec 22, 2008 at 9:47 AM, <drnevich at="" illinois.edu=""> wrote: > >> Hi Omri, >> >> I am already on vacation, so I won't be able to help you much until Dec. >> 30th. It is weird that you have to subset your list of probesets - >> something's not right there. I've never tried doing the RemoveProbes() more >> than once, so there also may be a problem there. You should be able to >> remove both probesets and individual probes in the same line. Try this: just >> do one set of RemoveProbes(), then immediately try to do rma. Do you still >> get the same error? If so, send me the list of probesets and probes that >> you want to remove. I'll download some yeast2 arrays to practice on when I >> get back. >> >> Sorry I can be of more help now, >> Jenny >> >> ---- Original message ---- >> >Date: Sat, 20 Dec 2008 20:36:50 +1300 >> >From: "Omri Yahel" <omri.yahel at="" gmail.com=""> >> >Subject: Fwd: [BioC] RMA error in cdf environment with removed probes >> (Yeast2) >> >To: drnevich at illinois.edu >> > >> > Hello Jenny >> > Sorry to bother you by sending you this email >> > directly, especially so close to christmas! It just >> > seemed you knew what you were talking about and i >> > wanted to make sure you got the response. My >> > apologies if you have already seen it. >> > Many thanks >> > Omri >> > >> > ---------- Forwarded message ---------- >> > From: Omri Yahel <omri.yahel at="" gmail.com=""> >> > Date: Thu, Dec 18, 2008 at 1:53 PM >> > Subject: Re: [BioC] RMA error in cdf environment >> > with removed probes (Yeast2) >> > To: bioconductor at stat.math.ethz.ch >> > >> > here is the code for the issue I am having. >> > Thanks again for you help >> > >> > > >> > > length(pm(data[,1])) >> > [1] 120855 >> > > >> > > >> > > #############remove selected S. cerevisiae probe >> > Ids >> > > >> > > >> > > >> > > source("RemoveProbesNew.r") >> > > library(yeast2cdf) >> > > library(yeast2probe) >> > > cleancdf <- cleancdfname("yeast2",addcdf=FALSE) >> > > ResetEnvir(cleancdf) >> > Loading required package: yeast2cdf >> > Loading required package: yeast2probe >> > > >> > > >> > RemoveProbes(listOutProbes[1:233],listOutProbeSets=NULL, >> > cleancdf) >> > > >> > RemoveProbes(listOutProbes[233:467],listOutProbeSets=NULL, >> > cleancdf) >> > > >> > RemoveProbes(listOutProbes[467:500],listOutProbeSets=NULL, >> > cleancdf) >> > > >> > RemoveProbes(listOutProbes[500:600],listOutProbeSets=NULL, >> > cleancdf) >> > > >> > RemoveProbes(listOutProbes[600:640],listOutProbeSets=NULL, >> > cleancdf) >> > > >> > RemoveProbes(listOutProbes[640:650],listOutProbeSets=NULL, >> > cleancdf) >> > > >> > RemoveProbes(listOutProbes[650:700],listOutProbeSets=NULL, >> > cleancdf) >> > > >> > RemoveProbes(listOutProbes[700:710],listOutProbeSets=NULL, >> > cleancdf) >> > > >> > RemoveProbes(listOutProbes[710:720],listOutProbeSets=NULL, >> > cleancdf) >> > > >> > RemoveProbes(listOutProbes[720:800],listOutProbeSets=NULL, >> > cleancdf) >> > > >> > RemoveProbes(listOutProbes[800:884],listOutProbeSets=NULL, >> > cleancdf) >> > > length(pm(data[,1])) >> > [1] 119991 >> > > >> > >######listOutProbes is a character vector of probe >> > ID's. I don't know why I had to subset it like this, >> > putting the >> > >######whole vector in, or larger subsets gave; >> > >######> >> > RemoveProbes(listOutProbes,listOutProbeSets=NULL, >> > cleancdf) >> > ####### Error in ans[[i]][, i.probes] : incorrect >> > number of dimensions >> > > >> > > >> > > >> > > >> > > >> > >############remove s. pombe probesets >> > > >> > > >> > > >> > > s_cerevisiae<-scan("s_cerevisiae.msk", skip=2, >> > list("", "")) >> > Read 5028 records >> > > pombe_filter_out<-s_cerevisiae[[1]] #the >> > probesets you DONT want. >> > > >> > > >> > > source("RemoveProbesNew.r") >> > > library(yeast2cdf) >> > > library(yeast2probe) >> > > cleancdf <- cleancdfname("yeast2",addcdf=FALSE) >> > > RemoveProbes(listOutProbes=NULL, pombe_filter_out, >> > cleancdf) >> > > length(pm(data[,1])) >> > [1] 64688 >> > ? >> > > >> > >#################################read in the new >> > data and do the RMA >> > > >> > > >> > > >> > pd<-read.AnnotatedDataFrame("targets.txt",header=TRUE,row.names=1, >> as.is=TRUE) >> > # reads the names from the targets file >> > > data <- >> > ReadAffy(filenames=pData(pd)$FileName,phenoData=pd) >> > # reads all .CEL files in the working directory and >> > assigns them names from the target files >> > > >> > > eset <- rma(data)#does the normalisation >> > Background correcting >> > Normalizing >> > Calculating Expression >> > Error in rma(data) : length of 'dimnames' [1] not >> > equal to array extent >> > > >> > > >> > > >> > > >> > > traceback() >> > 2: .Call("rma_c_complete", pm(object, subset), >> > pNList, ngenes, normalize, >> > background, bgversion, verbose, PACKAGE = >> > "affy") >> > 1: rma(data) >> > > >> > > >> > > >> > > >> > > sessionInfo() >> > R version 2.8.0 (2008-10-20) >> > i386-pc-mingw32 >> > >> > locale: >> > LC_COLLATE=English_New >> > Zealand.1252;LC_CTYPE=English_New >> > Zealand.1252;LC_MONETARY=English_New >> > Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New >> > Zealand.1252 >> > >> > attached base packages: >> > [1] tools stats graphics grDevices >> > utils datasets methods >> > [8] base >> > >> > other attached packages: >> > [1] yeast2probe_2.3.0 yeast2cdf_2.3.0 >> > matchprobes_1.14.0 >> > [4] yeast2.db_2.2.5 RSQLite_0.7-1 >> > DBI_0.2-4 >> > [7] AnnotationDbi_1.4.2 affy_1.20.0 >> > Biobase_2.2.1 >> > [10] limma_2.16.3 >> > >> > loaded via a namespace (and not attached): >> > [1] affyio_1.10.1 preprocessCore_1.4.0 >> > > >> > >> > Omri Yahel >> > >> > On Thu, Dec 18, 2008 at 4:04 AM, Jenny Drnevich >> > <drnevich at="" illinois.edu=""> wrote: >> > >> > Hi Omri, >> > >> > I'm assuming that the RemoveProbes.r function is >> > the one I have posted to the Bioconductor mailing >> > list several times, mostly recently with some >> > changes on Sept 24, 2008? >> > >> https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html >> > >> > If so, would you post your entire session, >> > including the code you used to remove the probe >> > sets and probes, along with your sessionInfo()? >> > That should give us more details so we can help >> > you. >> > >> > Thanks, >> > Jenny >> > >> > At 10:08 PM 12/16/2008, Omri Yahel wrote: >> > >> > Hello >> > >> > I am encountering an error during RMA of an >> > affybatch. >> > I have used RemoveProbes.r to remove all S. >> > pombe probesets and 864 >> > individual S.cerevisiae probes from the yeast2 >> > platform. >> > >> > >data<-ReadAffy() >> > > data >> > AffyBatch object >> > size of arrays=496x496 features (11 kb) >> > cdf=Yeast_2 (5900 affyids) >> > number of samples=26 >> > number of genes=5900 >> > annotation=yeast2 >> > notes= >> > > >> > > length(pm(data[,1])) >> > [1] 64688 >> > >> > When I attempt to compute the eset >> > >> > > eset <- rma(data) >> > Background correcting >> > Normalizing >> > Calculating Expression >> > Error in rma(data) : length of 'dimnames' [1] >> > not equal to array extent >> > >> > I assume this has something to do with the >> > removal of individual probes from >> > the environment, but am not sure and do not know >> > how to remedy this. >> > Any help appreciated >> > >> > Omri Yahel >> > MSc student >> > School of Biological Sciences >> > University of Auckland, New Zealand >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > Jenny Drnevich, Ph.D. >> > >> > Functional Genomics Bioinformatics Specialist >> > W.M. Keck Center for Comparative and Functional >> > Genomics >> > Roy J. Carver Biotechnology Center >> > University of Illinois, Urbana-Champaign >> > >> > 330 ERML >> > 1201 W. Gregory Dr. >> > Urbana, IL 61801 >> > USA >> > >> > ph: 217-244-7355 >> > fax: 217-265-5066 >> > e-mail: drnevich at illinois.edu >> Jenny Drnevich, Ph.D. >> Functional Genomics Bioinformatics Specialist >> Roy J. Carver Biotechnology Center >> University of Illinois, Urbana-Champaign >> >> 330 ERML >> 1201 W. Gregory Dr. >> Urbana, IL 61801 >> >> ph: 217-244-7355 >> fax: 217-265-5066 >> e-mail: drnevich at uiuc.edu >> > >